Coursework - Advanced Data Science - CMM536¶
- Surya L Ramesh (0206793)¶
Introduction:¶
The mask-mandate for protection against the COVID-19 pandemic has affected the field of facial recognition, where a need has risen to recognise faces with masks on. Efficient recognition systems are expected to check that faces are masked in regulated areas. This coursework is focuses on the facial recognition used to check if the detected face is correctly masked or unmasked, which can help with the enforcing the mask mandate. As an added level of complexity, this coursework looks at detecting incorrectly placed masks as well. Many people do not wear the masks correctly simply due to bad practice, lack of understanding or due to vulnerabilities of individuals. The class labels for this classification task have been chosen as:
- Unmasked
- CorrectlyMasked
- IncorrectlyMasked
Task 1: Data Compilation ¶
Keeping the three class labels in mind, a search was carried out for suitable images.
The Unmasked dataset was created from the Flickr-Faces-HQ(FFHQ) which contains high quality images of human faces and was created as a benchmark for generative adversarial networks (GAN).This dataset contains a good variation in terms of age, ethnicity and also variation of accessories like hats and glasses which the model can learn from. The Masked and Incorrectly masked data was compiled from MaskedFace-Net contains images of human faces with a correctly or incorrectly worn mask (133,783 images) based on the FFHQ dataset mentioned above. Masks have been artificially applied to the FFHQ dataset according to the categories.
Incorrectly Masked contains 3 sub-categories:
- Uncovered nose *chosen as IncorrectlyMasked
- Uncovered chin
- Uncovered nose and mouth.
For the purposes of this coursework the granularity of the of the dataset is not exploited to the fullest extent, as the Incorrectly Masked currently contains only 'Uncovered nose' images, as it is the mostly commonly found in real life.This is because this project is considered as a first step in experimentation and not a final solution.
The incorrectly labelled and unclear images were removed. The masked and incorrectly masked images of children under 3 were removed as well, as it is an impractical scenario.Then 2000 of each of the three categories was chosen for a range of ethnicity,ages and accessories.
Final Selection: The data was imbalanced to simulate real conditions, through code. The sizes now are:
- Unmasked: 1000
- CorrectlyMasked: 800
- IncorrectlyMasked: 100
The Layout of the experiments and the submitted files are shown below.
In [1]:
# Libraries
import os
import matplotlib.pyplot as plt
import matplotlib
import numpy as np
import cv2
import random
import pandas
import csv
import tensorflow as tf
from pandas import DataFrame
from sklearn.model_selection import train_test_split
from skimage.filters import try_all_threshold
from skimage.restoration import denoise_bilateral
from skimage.filters import sobel
from sklearn import svm
from sklearn.metrics import classification_report,accuracy_score
from sklearn.metrics import roc_auc_score
from sklearn.preprocessing import StandardScaler
from sklearn.decomposition import PCA
from sklearn.svm import SVC
import sys
import clustData
import computeKVs
import numpy as np
import csv
import math
import pandas as pd
import seaborn as sns
import numpy as np
import matplotlib.pyplot as plt
from keras.utils import np_utils
from sklearn.preprocessing import LabelEncoder
from sklearn.metrics import confusion_matrix
from sklearn import metrics
from imblearn.over_sampling import SMOTE
from imblearn.over_sampling import ADASYN
from sklearn.model_selection import StratifiedShuffleSplit
from termcolor import colored
import MyModels
In [2]:
# common functions
In [3]:
# function to show images
def show_image(image, title='Image', cmap_type='gray'):
plt.imshow(image, cmap=cmap_type)
plt.title(title)
plt.axis('off')
plt.show()
In [4]:
# function to display multiple images with titles
from PIL.Image import Image as PilImage
import textwrap
def display_images(imageset_array, titles, width=20, height=8, max_images=11,
label_wrap_length=50, label_font_size=8):
columns=len(imageset_array);
first_imageset = imageset_array[0]
if not first_imageset:
print("No images to display.")
return
if len(first_imageset) > max_images:
print(f"Showing {max_images} images of {len(first_imageset)}:")
first_imageset=first_imageset[0:max_images]
height = max(height, int(len(first_imageset)) * height)
plt.figure(figsize=(width, height))
for i, image in enumerate(first_imageset):
for j, imageset in enumerate(imageset_array):
plt.subplot(max_images, columns, i*columns+j+1)
plt.imshow(imageset[i],cmap='gray')
title=titles[j]
title=textwrap.wrap(title, label_wrap_length)
plt.title(title, fontsize=label_font_size);
In [5]:
# function to save flattened data as .csv
def save_CSV(filename,flattened_data,target):
print('\nSaving datasets as .csv files...')
with open(filename, 'w', newline='', encoding='utf-8') as csvfile:
filewriter = csv.writer(csvfile, delimiter=',')
for i, pix in enumerate(flattened_data):
row = np.concatenate((pix,[target[i]]))
filewriter.writerow(row)
print('\nData saved into .csv files!')
Task 2: Data Pre-processing¶
Task 2.1: Loading the Dataset and Original Repo ¶
In [6]:
# 2.11 loading the data
resize_width = 200 # chosen dimensions for the image
resize_height= 200 # chosen dimensions for the image
path = 'Data'
images = [] # List to append the images as 2D numpy arrays
target = [] # List for storing the 'class'
originalrepo = [] # Create a repo for flattened pixels
images_by_class = {} # Dictionary of images grouped by class
num_um = 1000 # set number of images in unmasked
num_cm = 800 # set number of images in correctly masked
num_in = 100 # set number of images in incorrectly masked
images_limit = { 'UnMasked':num_um,
'CorrectlyMasked':num_cm ,
'IncorrectlyMasked':num_in,
}
dirList = os.listdir(path)
for dir in dirList:
sub_path = os.path.join(path, dir)
for dirpath, dirnames, filenames in os.walk(sub_path):
n= images_limit.get(dir)
#print(n)
for filename in [f for f in filenames ][:n]:
#print (os.path.join(sub_path,filename))
img = cv2.imread(os.path.join(sub_path,filename), cv2.IMREAD_GRAYSCALE) # images read as grayscale for this project
img = cv2.resize(img, (resize_width, resize_height))
images.append(img)
# Append the flattened image to the pixel repo
originalrepo.append(img.flatten())
# Append the folder where the image is to the target list
className = dir
target.append(className)
#Group images by className
if className in images_by_class:
images_by_class[className].append(img.flatten())
else:
images_by_class[className] = [img.flatten()]
#save_CSV('Original.csv',originalrepo,target) # commented out to save time
In [7]:
# 2.12 View the repository created
# Convert the repo list into numpy array
originalrepo_np = np.array(originalrepo)
#print(originalrepo) # commented out for clarity
#print(target) # commented out for clarity
# Convert the repo list into pandas dataframe
originalrepowtarget = DataFrame(originalrepo)
originalrepowtarget['class']=DataFrame(target)
originalrepowtarget.head(5) # display first 5 lines
Out[7]:
In [8]:
# confirm shape of original repo
originalrepo_np.shape
Out[8]:
In [9]:
# 2.13 Confirming the distribution of the classes and exploration of the data
# How to display the total categories - summary or count?
originalrepowtarget['class'].value_counts()
#shows an inbalanced classes in our dataset
Out[9]:
In [10]:
# view the count in each class
plt.figure(figsize =((20,10)))
originalrepowtarget['class'].value_counts().sort_index().plot.barh(title = "Count of each category in the Dataset",color=['olive','rosybrown', 'darkturquoise'])
Out[10]:
In [11]:
# show sample image from the flattened original repo here
originalrepo[10]
Out[11]:
In [12]:
# choose one image from each class for display
index1 = len(images_by_class['CorrectlyMasked'])-2
index2 = index1 + len(images_by_class['IncorrectlyMasked'])-2
index3 = index2 + len(images_by_class['UnMasked'])-2
sample = [[images[index1]],[images[index2]],[images[index3]]]
# call display function to view the images
display_images(sample,["Correctly Masked ","Incorrectly Masked ","Unmasked"],max_images=3)
******* END OF DATA LOADING SECTION *******Task 2.2: Pre-processed Repository ¶
In [14]:
# function for just sobel
def filter_sobel(image):
sobel_image = sobel(image)
return sobel_image
In [15]:
# function to apply denoising then filter
def denoising_filter(image):
denoised_original = denoise_bilateral(image,multichannel=False)
sobel_original = sobel(image)
denoised_sobel = sobel(denoised_original)
return denoised_sobel
In [16]:
# function to apply filtering then denoise
def filter_denoising(image):
sobel_original = sobel(image) # apply sobel edge filtering
denoised_orginal = denoise_bilateral(image,multichannel=False)
sobel_denoised = denoise_bilateral(sobel_original,multichannel=False)
return sobel_denoised
In [17]:
#function for preprocessing - filter + denoising and add to repo
def Preprocess_repo(image):
sobel_original = sobel(image) # apply sobel edge filtering
sobel_denoised = denoise_bilateral(sobel_original,multichannel=False)
PP_repo.append(sobel_denoised) #apply denoising
PP_repoflatten.append(sobel_denoised.flatten()) # flatten the repo
2.21 Experimenting with Sobel Edge detection and Denoising¶
To compensate for loss of resolution due to cropping, sobel edge detection is used to extract the structures in the images. The aim is to focus on the features needed rather than the background or other distractions.Combining denoising which suppresses noise with sobel is done to check if the unnecessary details can be smoothed out to help with the classification.
In [18]:
# Apply sobel to limited number of images
n = 0
sobel_image = []
for x in images:
if n > 3:break # only first two images chosen for display
sobel_image.append(filter_sobel(x))
n = n+1
In [19]:
# Apply denoising + sobel to limited number of images
n = 0
denoised_filtered = []
for x in images:
if n > 3:break # only first two images chosen for display
denoised_filtered.append(denoising_filter(x))
n = n+1
In [20]:
# Apply edge detection sobel + denoising (reverse order) to limited number of images
n = 0
filtered_denoised = []
for x in images:
if n > 3:break # only first two images chosen for display
filtered_denoised.append(filter_denoising(x))
n = n+1
2.22 Choose Pre-processing method¶
Comparing the outputs of both the pre-processing steps above - it was decided to go with Filter +Denoised as it provided clarity while reducing noise.
In [21]:
# display limited number of images from the above experminent
display_images([sobel_image,denoised_filtered,filtered_denoised],["Just Sobel Filter","Denoised + Sobel Filter","Sobel Filter + Denoised"],max_images=3)
2.23 Apply the chosen method and create a pre-processed repository¶
In [22]:
# apply pre-processing and save the flattened file as csv
PP_repo =[]
PP_repoflatten=[]
for x in images:
Preprocess_repo(x) # call function to apply chosen preprocessing
print('Chosen Preprocessing is completed!')
print('Preprocessed file is flattened!')
save_CSV('Preprocessed.csv',PP_repoflatten,target) # call function to save as csv,can be commented out to save time
******* END OF PRE-PROCESSING SECTION *******Task 2.3: Feature Extraction Repository ¶
In feature extraction, a simplified representation of the image is created that contains only the most important information.Histograms of Oriented Gradients(HOG) is a type of feature extraction which is widely used in object and human detection as seen in Histograms of Oriented Gradients for Human Detection
To reduce the computational burden, HOG has been used to extract the features and then Principal Component Analysis (PCA) is applied to reduce the dimensions of the extracted features. This paper,HOG feature descriptor based PCA with SVM for efficient & accurate classification of objects in images shows that the HOG with PCA along with SVM produced the best results.
Hence,HOG + PCA is going to be applied to all the images.
In [23]:
# libraries for this section
from skimage.feature import hog
from skimage import exposure
In [24]:
# HOG function
def FE_Hog_flattened(x):
img_features = x.flatten()
fd, hog_image = hog(x, orientations=20, pixels_per_cell=(15, 15),
cells_per_block=(1, 1), visualize=True, multichannel=False)
flat_features = np.hstack([img_features,fd])
return flat_features,hog_image
2.31 Apply Histogram of Oriented Gradients (HOG) to Data¶
In [25]:
# apply the chosen Feature Extraction (HOG) to the to flattened images
HOG_repo = []
HOG_repoflatten =[]
HOG_features=[]
for x in images:
image_features,hog_image = FE_Hog_flattened(x) # call HOG function
HOG_features.append(image_features) # append features
HOG_repo.append(hog_image) # append to repo
# convert list of arrays into a matrix
feature_matrix = np.array(HOG_features) # create a matrix of features
In [26]:
# display images to verify
display_images([images,HOG_repo],["Original","with HOG"], max_images=2)
3.32 Apply Principal Component Analysis (PCA)¶
In [27]:
# Scale feature matrix + PCA
# get shape of feature matrix
print('Feature matrix shape is: ', feature_matrix.shape)
ss = StandardScaler() # define standard scaler
HOG_stand = ss.fit_transform(feature_matrix) # run standard scaler on our feature matrix
pca = PCA(n_components=40)
HOG_pca = pca.fit_transform(HOG_stand) # run PCA on the standardized matrix
print('PCA matrix shape is: ', HOG_pca.shape) # look at new shape
******* END OF FEATURE EXTRACTION SECTION *******Task 2.4: Augmented Repository ¶
Of the Data Augmentation techniques possible, geometric transformations - Horizontal reflection (HR) and translation(TR), have been chosen as they have been demonstrated to show some improvement in accuracy for emotion detection in this paper:Evaluation of Data Augmentation Techniques for Facial Expression Recognition Systems .
In [28]:
# function for augmentation
# border value chosen as 126 for a gray colour rather teh automatically chosen black '0', white '255'
def flip_translate(image, shift_x, shift_y):
flipped = cv2.flip(image,1) #5 '1' is for horizontal flip
# shifted along x and y axis
matrix = np.float32([[1, 0, shift_x], [0, 1, shift_y]])
ft_return = cv2.warpAffine(flipped , matrix , (flipped.shape[1], flipped.shape[0]),borderValue = 126)
return ft_return
In [29]:
# 2.41, 2.42 - sections for horizontal flip and translate combined into one
Augmented_repo = []
Augmented_repoflatten =[]
Augmented_target =[]
for i in range(len(images)):
r = images[i].copy()
Augmented_repo.append(r)
Augmented_repoflatten.append(r.flatten())
Augmented_target.append(target[i])
Aug= flip_translate(r,25,10)
Augmented_repo.append(Aug)
Augmented_repoflatten.append(Aug.flatten())
Augmented_target.append(target[i])
print('\nAugmentation is applied!\n')
print('\nSample augmented repo:\n')
Augmented_repo[0]
Out[29]:
In [30]:
print('\nSample augmented target:\n')
Augmented_target[0]
Out[30]:
In [31]:
# display sample images
display_images([Augmented_repo],["This repo contains Original and Augmented (HP + Translate) Images"], max_images=2)
In [32]:
#check size of repos now - the size should have doubled
print('\n The original repo length: ',len(originalrepo))
print('\n Augmented repo length: ',(len(Augmented_repo)))
print('\n The Augmented target length: ',(len(Augmented_target)))
******* END OF AUGMENTED SECTION *******Task 2.5: Class Decompositon and Syntetic minority oversampling (CDSMOTE) repository ¶
CDSMOTE is a new hybrid approach to correcting class imbalance. The proposed idea is a combination of under-sampling the majority class by class decomposition (CD) and oversampling the minority class by SMOTE. This reduces the dominance of majority class without information loss.
The code for this section is an adaptation of https://github.com/carlosfmorenog/CDSMOTE-BINARY/blob/master/demo.ipynb
In [33]:
# Functions for CD-SMOTE
In [34]:
# function for plotting clusters (before CD)
def plot_precluster(target,maj_class,min_class):
sns.set(style = "whitegrid")
# Plot distribution
plt.figure(figsize =((15,10)))
histo = [['Class','Number of Samples']]
for i, label1 in enumerate(sorted(list(set(target)))):
cont = 0
for j, label2 in enumerate(target):
if label1 == label2:
cont+=1
histo.append([label1,cont])
histo.append(['Total Samples', len(target)])
histo_panda = pd.DataFrame.from_records(histo[1:-1], columns=histo[0])
print(histo_panda)
print('Total samples: '+str(len(target)))
## Find IR
majority_samples = histo_panda.loc[histo_panda['Class'] == maj_class].reset_index()
minority_samples = histo_panda.loc[histo_panda['Class'] == min_class].reset_index()
IR = majority_samples['Number of Samples'][0]/minority_samples['Number of Samples'][0]
print('Imbalance Ratio (IR): '+str(IR))
print(majority_samples)
## Create a histogram using seaborn
#sns.set_palette("prism")
sns_plot = sns.barplot(x="Class", y="Number of Samples", data=histo_panda)
In [35]:
# function for class decompositon
def decompose_class ( data,target,n_clust=4):
sns.set(style = "whitegrid")
#n_clusters = 4
plt.figure(figsize =((15,10)))
## Calculate k vector (for class decomposition)
if k_type.lower() == 'fixed':
k = computeKVs.majority(data, target, n_clust)
elif k_type.lower() == 'ir':
## Calculate the IR between the majority and the minority
n_clusters = math.ceil(IR)
k = computeKVs.majority(data, target,n_clust)
else:
print('Invalid option for k_type')
sys.exit()
print(k)
## 2. Cluster the data
if classdecomp.lower()=='kmeans':
target_cd = clustData.Kmeans(data, target, k)
elif classdecomp.lower()=='fcmeans':
target_cd = clustData.FCmeans(data, target, k)
elif classdecomp.lower()=='fcmeansoptimised':
target_cd = clustData.FCmeansOptimised(data, target, k, max_nclusters = 10)
elif classdecomp.lower()=='dbscan':
target_cd = clustData.DBSCAN(data, target, k, eps=0.5, min_samples=5)
else:
print('Invalid class decomposition algorithm.')
sys.exit()
return target_cd ##return
In [36]:
# function for plotting clusters (after CD)
def plot_postcluster(target_cd):
sns.set(style = "whitegrid")
plt.figure(figsize =((20,10)))
histo = [['Class','Number of Samples']]
for i, label1 in enumerate(sorted(list(set(target_cd)))):
cont = 0
for j, label2 in enumerate(target_cd):
if label1 == label2:
cont+=1
histo.append([label1,cont])
histo.append(['Total Samples', len(target_cd)])
## Load as a panda
histo_panda = pd.DataFrame.from_records(histo[1:-1], columns=histo[0])
print(histo_panda)
print('Total samples: '+str(len(target_cd)))
## Create a histogram using seaborn
#sns.set_palette("prism")
sns_plot = sns.barplot(x="Class", y="Number of Samples",data=histo_panda)
## draw a line depicting the average
indexesUnique = list(set(target_cd))
indexesUnique.sort()
cdclassdist_count = []
cdclassdist_names = []
for cdclass in indexesUnique:
cdclassdist_count.append(target_cd.count(cdclass))
cdclassdist_names.append(cdclass)
average = sum(cdclassdist_count)/len(cdclassdist_count)
print('Average number of samples per class:', average)
plt.axhline(average, color='red')
return cdclassdist_count,cdclassdist_names
In [37]:
def get_minority_majority(data_dictionary):
longest = max(len(item) for item in data_dictionary.values())
majority_class = [key for key, value in data_dictionary.items() if len(value) == longest]
smallest = min(len(item) for item in data_dictionary.values())
minority_class = [key for key, value in data_dictionary.items() if len(value) == smallest]
return majority_class[0], minority_class[0];
In [38]:
dataset = 'C15' # name of the dataset to use. C1-31 are binary datasets presented in Cleofas-Sanchez et al. 2016
classdecomp = 'Kmeans' # 'FCmeans', 'FCmeansOptimised' and 'DBSCAN' also available
oversampler = 'SMOTE' #'ADASYN' also available
threshold = 10 # if samples in positive class are apart from average by more than this value, apply oversampling (Sec 3.2 paper)
k_type = 'fixed' # Indicates how to calculate k values for class decomposition
n_clusters = 4 # used in the "fixed" k_type option # passing in functio instead of here
number_of_tests = 5 # How many times to repeat the SVM experiment comparing the original and new db
#NOTE: Class decomposition only finds clusters of data , similar to other data.
#To evaluate the model the decomposed classes has been added together.
In [39]:
# apply CDSMOTE
In [40]:
# applying class decomposition
original_images_by_class = images_by_class.copy()
majority_class = max(set(target), key=target.count)
minority_class = min(set(target), key=target.count)
images_to_process = images_by_class[majority_class].copy()
images_to_process.extend(images_by_class[minority_class])
targets_to_process = [majority_class] * len(images_by_class[majority_class])
targets_to_process.extend([minority_class] * len(images_by_class[minority_class] ))
# This section is for debugging/ additional information- Commented out for clarity
#print(len(images_by_class[majority_class]))
#print(len(images_by_class[minority_class]))
#print(len(images_by_class["CorrectlyMasked"]))
#print(len(targets_to_process))
#print(len(images_to_process))
#print(targets_to_process)
In [41]:
plot_precluster(targets_to_process,majority_class,minority_class)
In [42]:
#decompose the classes
cdclassdist_count_1=[]
cdclassdist_names_1=[]
clustered_1 = decompose_class(images_to_process,targets_to_process,n_clusters)
cdclassdist_count_1,cdclassdist_names_1=plot_postcluster(clustered_1)
In [43]:
#remove the already decomposed class
new_images_by_class = original_images_by_class.copy()
new_images_by_class.pop(majority_class)
new_majority_class, minority_class = get_minority_majority(new_images_by_class)
new_images_to_process = new_images_by_class[new_majority_class].copy()
new_images_to_process.extend(new_images_by_class[minority_class])
new_targets_to_process = [new_majority_class] * len(new_images_by_class[new_majority_class])
new_targets_to_process.extend([minority_class] * len(new_images_by_class[minority_class] ))
In [44]:
plot_precluster(new_targets_to_process,new_majority_class,minority_class)
In [45]:
cdclassdist_count_2=[]
cdclassdist_names_2=[]
clustered_2 = decompose_class(new_images_to_process,new_targets_to_process,n_clusters)
cdclassdist_count_2,cdclassdist_names_2=plot_postcluster(clustered_2)
In [46]:
# Join the two clustured sets together and display as one
clust = []
clustered_2 = [x for x in clustered_2 if not x.startswith(minority_class)]
clust = clustered_1.copy()
clust.extend(clustered_2)
plot_postcluster(clust)
cdclassdist_names = cdclassdist_names_1.copy()
for i in range(len(cdclassdist_names_2)):
if cdclassdist_names_2[i].startswith(minority_class):
del cdclassdist_names_2[i]
del cdclassdist_count_2[i]
cdclassdist_names.extend(cdclassdist_names_2)
cdclassdist_count = cdclassdist_count_1.copy()
cdclassdist_count.extend(cdclassdist_count_2)
average = sum(cdclassdist_count)/len(cdclassdist_count)
print('Average number of samples per class in the combined:', average)
print(cdclassdist_count)
print(cdclassdist_names)
In [47]:
# apply SMOTE section
In [48]:
plt.figure(figsize =((20,10)))
## 1. See if the minority is far from the average (larger than the threshold)
flag = 0
for i,cdclassdist_name in enumerate(cdclassdist_names):
if minority_class == cdclassdist_name.split('_')[0]:
if abs(average-cdclassdist_count[i])>threshold and average>cdclassdist_count[i]:
flag = 1
newmin = cdclassdist_name
if flag ==1:
print('Oversampling original minority class...')
## 2. Calculate new majority class (closest to the average and larger than the minority) to use as reference for the oversampling
c = np.inf
newmaj = majority_class + '_c0' # gets picked by default if none other accomplishes
for i,j in enumerate(cdclassdist_count):
if abs(j-average)<c and j>average:
c = abs(j-average)
newmaj = cdclassdist_names[i]
## 3. Create the dataset that only contains the new majority and minority classes
data_majmin = []
target_majmin = []
for m, label in enumerate(clust):
if label == newmaj or label == newmin:
data_majmin.append(originalrepo[m])
target_majmin.append(label)
if oversampler.lower() == 'smote':
sm = SMOTE()
data_over, target_over = sm.fit_resample(data_majmin, target_majmin)
elif oversampler.lower() == 'adasyn':
ada = ADASYN()
data_over, target_over = ada.fit_resample(data_majmin, target_majmin)
else:
print('Invalid oversampling algorithm.')
sys.exit()
## 4. combine this with the remaining classes
data_cdsmote = data_over.copy()
target_cdsmote = target_over.copy()
for m, label in enumerate(clust):
if label != newmin and label != newmaj:
data_cdsmote.append(originalrepo[m])
target_cdsmote.append(label)
## 5. Plot distribution after smote
histo = [['Class','Number of Samples']]
for i, label1 in enumerate(sorted(list(set(target_cdsmote)))):
cont = 0
for j, label2 in enumerate(target_cdsmote):
if label1 == label2:
cont+=1
histo.append([label1,cont])
histo.append(['Total Samples', len(target_cdsmote)])
## Load as a panda
histo_panda = pd.DataFrame.from_records(histo[1:-1], columns=histo[0])
print(histo_panda)
print('Total samples: '+str(len(target_cdsmote)))
## Create a histogram using seaborn
sns_plot = sns.barplot(x="Class", y="Number of Samples", data=histo_panda)
## draw a line depicting the average
indexesUnique = list(set(target_cdsmote))
indexesUnique.sort()
newestclassdist_count = []
for newestclass in indexesUnique:
newestclassdist_count.append(target_over.count(newestclass))
average_new = sum(newestclassdist_count)/len(newestclassdist_count)
print('New average number of samples per class:', average_new)
plt.axhline(average, color='red')
plt.axhline(average_new, color='blue')
plt.show()
else:
data_cdsmote = originalrepo.copy()
target_cdsmote = clust.copy()
print('Original minority class is close to average. No oversampling needed.')
******* END OF CD-SMOTE SECTION *******Task 3: Data Classification and Evaluation ¶
The chosen classfiers are:
The training and testing framework is shown in Figure 3.
In [50]:
# NOTE-functions for the classifiers and hyperparameter tuning can be found in the Mymodels.py,attached to this coursework submission.
In [51]:
# libraries for this section
from sklearn.metrics import plot_confusion_matrix
from sklearn.metrics import ConfusionMatrixDisplay
from sklearn.metrics import accuracy_score
from yellowbrick.classifier import ROCAUC
import itertools
import numpy as np
import matplotlib.pyplot as plt
In [52]:
# function for confusion matrix - used for CNN and CD-SMOTE Repo
def plot_confusion_matrix_custom(cm, classes, normalize=False, title='Confusion matrix', cmap=plt.cm.Blues):
if normalize:
cm = cm.astype('float') / cm.sum(axis=1)[:, np.newaxis]
print("Normalized confusion matrix")
else:
print('Confusion matrix, without normalization')
print(cm)
plt.figure()
plt.imshow(cm, interpolation='nearest', cmap=cmap)
plt.title(title)
plt.colorbar()
tick_marks = np.arange(len(classes))
plt.xticks(tick_marks, classes, rotation=45)
plt.yticks(tick_marks, classes, rotation=45)
fmt = '.2f' if normalize else 'd'
thresh = cm.max() / 2.
for i, j in itertools.product(range(cm.shape[0]), range(cm.shape[1])):
plt.text(j, i, format(cm[i, j], fmt), horizontalalignment="center", color="white" if cm[i, j] > thresh else "black")
plt.ylabel('True label')
plt.xlabel('Predicted label')
plt.grid(None)
plt.show()
# code for this function is adapted from deeplizard.com
Classifiers(ADAboost,RF,SVC) and all suitable repos
In [53]:
# looping through classifiers(ADAboost , RF , SVC ) and all the repos
# make repos into a list
all_repos = [
('Original Repo' ,originalrepo,target),
('Pre-processed Repo',PP_repoflatten,target),
('HOG Repo',HOG_pca,target),
('Augmented Repo',Augmented_repoflatten,Augmented_target),
('CD-SMOTE Repo', data_cdsmote,target_cdsmote)
]
#split = [X_train,X_test, y_train, y_test,y_pred, y_predtrain] - for reference from MyModels.py
X_train_idx = 0
X_test_idx = 1
y_train_idx = 2
y_test_idx = 3
y_pred_idx = 4
y_predtrain_idx = 5
results_dict = []
split_list = []
models = []
train_scores = [] # new
test_scores =[] # new
for name,repo,targets in all_repos:
print("\n Processing ",name)
models = [MyModels.ADAboost_mod(repo,targets,split_list),
MyModels.RF(repo,targets,split_list),
MyModels.SVClinear(repo,targets,split_list)]
for i in range(len(split_list)):
splits = split_list[i]
model = models[i]
visualizer = ROCAUC(model)
visualizer.fit(splits[X_train_idx],splits[y_train_idx]) # Fit the visualizer and the model (X_train y_train)
visualizer.score(splits[X_test_idx],splits[y_test_idx]) # Evaluate the model on the test data (X_test y_test)
visualizer.poof()
print(colored("\n Accuracy -Check for generalisation... - for : %s\n"%(name),'green')) # new section
for i in range(len(split_list)):
model = models[i]
splits = split_list[i]
modelname = model.__class__.__name__
print(colored("\n %s\n"%(modelname),'green'))
# Append the accuracy score for the test and train predictions.
train_scores.append(round(accuracy_score(splits[y_train_idx], splits[y_predtrain_idx]), 2))
test_scores.append(round(accuracy_score(splits[y_test_idx], splits[y_pred_idx]), 2))
# Print the train and test scores.
print("The training scores were: {}".format(train_scores))
print("The testing scores were: {}".format(test_scores))
train_scores.clear()# new
test_scores.clear()
# print classification report
print(colored("\n The Classification Report for : %s\n"%(name),'green'))
for i in range(len(split_list)):
model = models[i]
splits = split_list[i]
modelname = model.__class__.__name__
y_test_c = []
y_pred_c = []
if(name == 'CD-SMOTE Repo'): #Join all subclasses for CD SMOTE
for i,label in enumerate(splits[y_test_idx]):
y_test_c.append(label.split('_')[0])
y_pred_c.append(splits[y_pred_idx][i].split('_')[0])
else :
y_test_c = splits[y_test_idx]
y_pred_c = splits[y_pred_idx]
print(colored("\n %s\n"%(modelname),'green'))
print(classification_report(y_test_c, y_pred_c, zero_division=1))
# plot Confusion Matrix
if(name == 'CD-SMOTE Repo'): #Join all subclasses for CD SMOTE
classes = ['CorrectlyMasked','IncorrectlyMasked','UnMasked']
for cls,i in zip(models, range(len(split_list))):
splits = split_list[i]
y_test_c = []
y_pred_c = []
for i,label in enumerate(splits[y_test_idx]):
y_test_c.append(label.split('_')[0])
y_pred_c.append(splits[y_pred_idx][i].split('_')[0])
confusion_matrix = metrics.confusion_matrix(y_test_c, y_pred=y_pred_c)
plot_confusion_matrix_custom(confusion_matrix,classes,title =type(cls).__name__,normalize=False)
else:
ncols=len(split_list)
fig, axes = plt.subplots(nrows=1, ncols=len(split_list), figsize=(30,10))
for cls, ax,i in zip(models, axes,range(len(split_list))):
splits = split_list[i]
plot_confusion_matrix(cls,
splits[X_test_idx],
splits[y_test_idx],
ax=ax,
cmap='Blues',
xticks_rotation='vertical')
ax.grid(False)
ax.set_title(type(cls).__name__, fontdict={'fontsize': 15, 'fontweight': 'bold'})
ax.set_yticklabels(ax.get_yticklabels(), rotation = 45, fontsize = 15)
ax.set_xticklabels(ax.get_xticklabels(), rotation = 45, fontsize = 15)
plt.tight_layout()
plt.show()
models.clear()
split_list.clear()
results_dict.clear()
Hyperparameter Tuning
As the model were showing signs of overfitting(the test was worser than train scores), the hyper parameters needs tuning. A faster way to tune is to use 'random searching',as discussed in Random Search for Hyper-Parameter Optimization. In this, a list of possible values is given and the values are randomly selected from it.A cross validation of 5 is used with random searching to determine the best model. Tuning was repeated with valid hyperparameters for each model till all the model outputs were generalising well.All code used for classifiers and hyperparameter tuning can be found in MyModels.py, attached to the coursework submission.
In [ ]:
**CNN for all repos**
Early stopping and callback was done for all repos and the best models have been used.Figure below shows the results for the original repo.
In [54]:
# looping through all repos with CNN
classes = ['CorrectlyMasked','IncorrectlyMasked','UnMasked']
all_repos1 = [
('Original Repo' ,originalrepo,target,'best_model_orig.h5'),
('Pre-processed Repo',PP_repoflatten,target,'best_model_pp.h5'),
('Augmented Repo',Augmented_repoflatten,Augmented_target,'best_model_aug.h5'),
('CD-SMOTE Repo', data_cdsmote,target_cdsmote,'best_model_cd.h5')
]
split_list = []
for name,repo,targets,saved_model_name in all_repos1:
print("\n\nProcessing for CNN : \n",name)
if (name =='CD-SMOTE Repo'):
labels=9
else:
labels=3
MyModels.CNN_mod(name, repo,targets,labels,saved_model_name,split_list)
# Print classification Reports for each Repo
for i in range(len(split_list)):
y_test_c = split_list[i][0]
y_pred_c = split_list[i][1]
print(colored("Classification Report for Repo:{}".format(all_repos1[i][0]),'green'))
print(classification_report(y_test_c, y_pred=y_pred_c,zero_division=1))
#Plot Confusion maatrix for each Repo
for i in range(len(split_list)):
y_test_c = split_list[i][0]
y_pred_c = split_list[i][1]
confusion_matrix = metrics.confusion_matrix(y_test_c, y_pred=y_pred_c)
plot_confusion_matrix_custom(confusion_matrix,classes, title= "Confusion Matrix for {}".format(all_repos1[i][0]))
In [ ]:
# # looping through all repos with CNN
# all_repos1 = [
# ('Original Repo' ,originalrepo,target,'best_model_orig.h5'),
# ('Pre-processed Repo',PP_repoflatten,target,'best_model_pp.h5'),
# ('Augmented Repo',Augmented_repoflatten,Augmented_target,'best_model_aug.h5'),
# ('CD-SMOTE Repo', data_cdsmote,target_cdsmote,'best_model_cd.h5')
# ]
# for name,repo,targets,saved_model_name in all_repos1:
# print("\n\nProcessing for CNN : \n",name)
# if (name =='CD-SMOTE Repo'):
# labels=9
# else:
# labels=3
# MyModels.CNN_mod(name, repo,targets,labels,saved_model_name)
Task 4: Final Reflection ¶
References:¶
All references have been added as hyperlinks in the relevant sections.
In [ ]: